Importing ArrayExpress datasets into R/Bioconductor

by Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, Huber, Wolfgang
Published 2009

Mutational landscape of a chemically-induced mouse model of liver cancer

by Connor, Frances, Rayner, Tim F., Aitken, Sarah J., Feig, Christine, Lukk, Margus, Santoyo-Lopez, Javier, Odom, Duncan T.
Published in J Hepatol (2018)

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB

by Rayner, Tim F., Rezwan, Faisal Ibne, Lukk, Margus, Bradley, Xiangqun Zheng, Farne, Anna, Holloway, Ele, Malone, James, Williams, Eleanor, Parkinson, Helen
Published 2009

Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type–specific hypomethylated regions

by Zilbauer, Matthias, Rayner, Tim F., Clark, Christine, Coffey, Alison J., Joyce, Chris J., Palta, Priit, Palotie, Aarno, Lyons, Paul A., Smith, Kenneth G. C.
Published 2013

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

by Wong, Emily S., Schmitt, Bianca M., Kazachenka, Anastasiya, Thybert, David, Redmond, Aisling, Connor, Frances, Rayner, Tim F., Feig, Christine, Ferguson-Smith, Anne C., Marioni, John C., Odom, Duncan T., Flicek, Paul
Published in Nat Commun (2017)

Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis

by Lyons, Paul A, McKinney, Eoin F, Rayner, Tim F, Hatton, Alexander, Woffendin, Hayley B, Koukoulaki, Maria, Freeman, Thomas C, Jayne, David R W, Chaudhry, Afzal N, Smith, Kenneth G C
Published 2010

Gene expression profiling of CD8(+) T cells predicts prognosis in patients with Crohn disease and ulcerative colitis

by Lee, James C., Lyons, Paul A., McKinney, Eoin F., Sowerby, John M., Carr, Edward J., Bredin, Francesca, Rickman, Hannah M., Ratlamwala, Huzefa, Hatton, Alexander, Rayner, Tim F., Parkes, Miles, Smith, Kenneth G.C.
Published 2011

Foxp3(+) follicular regulatory T cells control T follicular helper cells and the germinal center response

by Linterman, Michelle A., Pierson, Wim, Lee, Sau K., Kallies, Axel, Kawamoto, Shimpei, Rayner, Tim F., Srivastava, Monika, Divekar, Devina P., Beaton, Laura, Hogan, Jennifer J., Fagarasan, Sidonia, Liston, Adrian, Smith, Kenneth G. C., Vinuesa, Carola G.
Published 2011

Enhancer Evolution across 20 Mammalian Species

by Villar, Diego, Berthelot, Camille, Aldridge, Sarah, Rayner, Tim F., Lukk, Margus, Pignatelli, Miguel, Park, Thomas J., Deaville, Robert, Erichsen, Jonathan T., Jasinska, Anna J., Turner, James M.A., Bertelsen, Mads F., Murchison, Elizabeth P., Flicek, Paul, Odom, Duncan T.
Published in Cell (2015)

A defunctioning polymorphism in FCGR2B is associated with protection against malaria but susceptibility to systemic lupus erythematosus

by Willcocks, Lisa C., Carr, Edward J., Niederer, Heather A., Rayner, Tim F., Williams, Thomas N., Yang, Wanling, Scott, J. Anthony G., Urban, Britta C., Peshu, Norbert, Vyse, Timothy J., Lau, Yu Lung, Lyons, Paul A., Smith, Kenneth G. C.
Published 2010

MiR-210 is induced by Oct-2, regulates B-cells and inhibits autoantibody production()

by Mok, Yingting, Schwierzeck, Vera, Thomas, David C., Vigorito, Elena, Rayner, Tim F., Jarvis, Lorna B., Prosser, Haydn M., Bradley, Allan, Withers, David R., Mårtensson, Inga-Lill, Corcoran, Lynn M., Blenkiron, Cherie, Miska, Eric A., Lyons, Paul A., Smith, Kenneth G.C.
Published 2013

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

by Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, Irizarry, Rafael A, Liu, Junmin, Maier, Donald S, Miller, Michael, Petersen, Kjell, Quackenbush, John, Sherlock, Gavin, Stoeckert, Christian J, White, Joseph, Whetzel, Patricia L, Wymore, Farrell, Parkinson, Helen, Sarkans, Ugis, Ball, Catherine A, Brazma, Alvis
Published 2006

Copy number, linkage disequilibrium and disease association in the FCGR locus

by Niederer, Heather A., Willcocks, Lisa C., Rayner, Tim F., Yang, Wanling, Lau, Yu Lung, Williams, Thomas N., Scott, J. Anthony G., Urban, Britta C., Peshu, Norbert, Dunstan, Sarah J., Hien, Tran Tinh, Phu, Nguyen Hoan, Padyukov, Leonid, Gunnarsson, Iva, Svenungsson, Elisabet, Savage, Caroline O., Watts, Richard A., Lyons, Paul A., Clayton, David G., Smith, Kenneth G.C.
Published 2010

ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

by Parkinson, Helen, Kapushesky, Misha, Kolesnikov, Nikolay, Rustici, Gabriella, Shojatalab, Mohammad, Abeygunawardena, Niran, Berube, Hugo, Dylag, Miroslaw, Emam, Ibrahim, Farne, Anna, Holloway, Ele, Lukk, Margus, Malone, James, Mani, Roby, Pilicheva, Ekaterina, Rayner, Tim F., Rezwan, Faisal, Sharma, Anjan, Williams, Eleanor, Bradley, Xiangqun Zheng, Adamusiak, Tomasz, Brandizi, Marco, Burdett, Tony, Coulson, Richard, Krestyaninova, Maria, Kurnosov, Pavel, Maguire, Eamonn, Neogi, Sudeshna Guha, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sklyar, Nataliya, Zhao, Mengyao, Sarkans, Ugis, Brazma, Alvis
Published 2009

Pervasive lesion segregation shapes cancer genome evolution

by Aitken, Sarah J., Anderson, Craig J., Connor, Frances, Pich, Oriol, Sundaram, Vasavi, Feig, Christine, Rayner, Tim F., Lukk, Margus, Aitken, Stuart, Luft, Juliet, Kentepozidou, Elissavet, Arnedo-Pac, Claudia, Beentjes, Sjoerd V., Davies, Susan E., Drews, Ruben M., Ewing, Ailith, Kaiser, Vera B., Khamseh, Ava, López-Arribillaga, Erika, Redmond, Aisling M., Santoyo-Lopez, Javier, Sentís, Inés, Talmane, Lana, Yates, Andrew D., Semple, Colin A., López-Bigas, Núria, Flicek, Paul, Odom, Duncan T., Taylor, Martin S.
Published in Nature (2020)

Genetically Distinct Subsets within ANCA-Associated Vasculitis

by Lyons, Paul A., Rayner, Tim F., Trivedi, Sapna, Holle, Julia U., Watts, Richard A., Jayne, David R.W., Baslund, Bo, Brenchley, Paul, Bruchfeld, Annette, Chaudhry, Afzal N., Tervaert, Jan Willem Cohen, Deloukas, Panos, Feighery, Conleth, Gross, Wolfgang L., Guillevin, Loic, Gunnarsson, Iva, P, Lorraine Harper M.R.C, Hrušková, Zdenka, Little, Mark A., Martorana, Davide, Neumann, Thomas, Ohlsson, Sophie, Padmanabhan, Sandosh, Pusey, Charles D., Salama, Alan D., Sanders, Jan-Stephan F., Savage, Caroline O., Segelmark, Mårten, Stegeman, Coen A., Tesař, Vladimir, Vaglio, Augusto, Wieczorek, Stefan, Wilde, Benjamin, Zwerina, Jochen, Rees, Andrew J., Clayton, David G., Smith, Kenneth G.C.
Published 2012